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Port details
ddocent Bash pipeline for RAD sequencing
2.7.8_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 01:34:22
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: java perl5 python
License: MIT
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (22 items)
Collapse this list.
  1. /usr/local/share/licenses/dDocent-2.7.8_1/catalog.mk
  2. /usr/local/share/licenses/dDocent-2.7.8_1/LICENSE
  3. /usr/local/share/licenses/dDocent-2.7.8_1/MIT
  4. bin/ErrorCount.sh
  5. bin/RefMapOpt.sh
  6. bin/ReferenceOpt.sh
  7. bin/Rename_SequenceFiles.sh
  8. bin/Rename_for_dDocent.sh
  9. bin/Rename_for_dDocent_with-INDEX.sh
  10. bin/dDocent
  11. bin/dDocent_filters
  12. bin/dDocent_ngs.sh
  13. bin/ddocent-assembly-test
  14. bin/ddocent-assembly-test-cleanup
  15. bin/filter_hwe_by_pop.pl
  16. bin/filter_missing_ind.sh
  17. bin/pop_missing_filter.sh
  18. bin/remake_reference.sh
  19. bin/remove.bad.hap.loci.sh
  20. @owner
  21. @group
  22. @mode
Collapse this list.
Dependency lines:
  • dDocent>0:biology/ddocent
To install the port:
cd /usr/ports/biology/ddocent/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ddocent
  • pkg install dDocent
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: dDocent
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
dDocent
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.7.8_12.7.8_1
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3862.7.8_12.7.8_1
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd642.7.8_12.7.8_1
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd642.7.8_12.7.8_1
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd642.7.8_1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. mawk>=0 : lang/mawk
  2. gawk>=0 : lang/gawk
  3. coreutils>=0 : sysutils/coreutils
  4. gnuplot>=0 : math/gnuplot
  5. parallel>=0 : sysutils/parallel
  6. bash : shells/bash
  7. bwa>=0.7.13 : biology/bwa
  8. cd-hit>=0 : biology/cd-hit
  9. samtools>=1.3 : biology/samtools
  10. vcftools>=0.1.15 : biology/vcftools
  11. trimmomatic>=0 : biology/trimmomatic
  12. bamtools>=0 : biology/bamtools
  13. stacks>=0 : biology/stacks
  14. rainbow>=0 : biology/rainbow
  15. trimadap>=0 : biology/trimadap
  16. seqtk>=0 : biology/seqtk
  17. bedtools>=2.26.0 : biology/bedtools
  18. pear-merger>=0 : biology/pear-merger
  19. vcflib>=0 : biology/vcflib
  20. freebayes : biology/freebayes
  21. fastp : biology/fastp
  22. java : java/openjdk8
  23. python3.9 : lang/python39
  24. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/jpuritz/dDocent/tar.gz/v2.7.8?dummy=/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.7.8_1
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.7.8_1
30 Sep 2021 21:23:30
commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index
2.7.8_1
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.7.8_1
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.7.8_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
2.7.8
04 May 2019 15:09:10
Revision:500812Original commit files touched by this commit
jwb search for other commits by this committer
biology/ddocent: Upgrade to 2.7.8

Reported by:    portscout
2.2.25_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
2.2.25
20 Apr 2018 01:34:05
Revision:467808Original commit files touched by this commit
jwb search for other commits by this committer
biology/ddocent: Bash pipeline for RAD sequencing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15139

Number of commits found: 9